Related papers: A survey of BWT variants for string collections
Converting a compressed format of a string into another compressed format without an explicit decompression is one of the central research topics in string processing. We discuss the problem of converting the run-length Burrows-Wheeler…
In this paper, we consider the problem of compressing a trie while supporting the powerful \emph{locate} queries: to return the pre-order identifiers of all nodes reached by a path labeled with a given query pattern. Our result builds on…
Extracting meaningful features from complex, high-dimensional datasets across scientific domains remains challenging. Current methods often struggle with scalability, limiting their applicability to large datasets, or make restrictive…
Existing approaches for generating multitrack music with transformer models have been limited in terms of the number of instruments, the length of the music segments and slow inference. This is partly due to the memory requirements of the…
Extending computational harmonic analysis tools from the classical setting of regular lattices to the more general setting of graphs and networks is very important and much research has been done recently. The Generalized Haar-Walsh…
Despite the outstanding performance of transformers in both language and vision tasks, the expanding computation and model size have increased the demand for efficient deployment. To address the heavy computation and parameter drawbacks,…
Data subset selection aims to find a smaller yet informative subset of a large dataset that can approximate the full-dataset training, addressing challenges associated with training neural networks on large-scale datasets. However, existing…
This paper reveals that we can interpret the fundamental function of Randomized Time Warping (RTW) as a type of self-attention mechanism, a core technology of Transformers in motion recognition. The self-attention is a mechanism that…
The results obtained by analyzing signals with the Square Wave Method (SWM) introduced previously can be presented in the frequency domain clearly and precisely by using the Square Wave Transform (SWT) described here. As an example, the SWT…
We describe a grammar for DNA sequencing reads from which we can compute the BWT directly. Our motivation is to perform in succinct space genomic analyses that require complex string queries not yet supported by repetition-based…
Transformer-based models, exemplified by GPT-3, ChatGPT, and GPT-4, have recently garnered considerable attention in both academia and industry due to their promising performance in general language tasks. Nevertheless, these models…
The FM-index is a well-known compressed full-text index, based on the Burrows-Wheeler transform (BWT). During a pattern search, the BWT sequence is accessed at "random" locations, which is cache-unfriendly. In this paper, we are interested…
A degenerate or indeterminate string on an alphabet $\Sigma$ is a sequence of non-empty subsets of $\Sigma$. Given a degenerate string $t$ of length $n$, we present a new method based on the Burrows--Wheeler transform for searching for a…
Automatic drum transcription, a subtask of the more general automatic music transcription, deals with extracting drum instrument note onsets from an audio source. Recently, progress in transcription performance has been made using…
Cartesian tree matching is a form of generalized pattern matching where a substring of the text matches with the pattern if they share the same Cartesian tree. This form of matching finds application for time series of stock prices and can…
Time-frequency representations (TFRs) of signals, such as the windowed Fourier transform (WFT), wavelet transform (WT) and their synchrosqueezed variants (SWFT, SWT), provide powerful analysis tools. However, there are many important issues…
A Behavior Tree (BT) is a way to structure the switching between different tasks in an autonomous agent, such as a robot or a virtual entity in a computer game. BTs are a very efficient way of creating complex systems that are both modular…
String kernels are typically used to compare genome-scale sequences whose length makes alignment impractical, yet their computation is based on data structures that are either space-inefficient, or incur large slowdowns. We show that a…
String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…
We propose an external memory algorithm for the computation of the BWT and LCP array for a collection of sequences. Our algorithm takes the amount of available memory as an input parameter, and tries to make the best use of it by splitting…